Fam50a (family with sequence similarity 50, member A) - Rat Genome Database

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Gene: Fam50a (family with sequence similarity 50, member A) Rattus norvegicus
Analyze
Symbol: Fam50a
Name: family with sequence similarity 50, member A
RGD ID: 1560964
Description: Predicted to be involved in chromatin organization and regulation of RNA splicing. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Armfield syndrome. Orthologous to human FAM50A (family with sequence similarity 50 member A); INTERACTS WITH alpha-Zearalanol; amphetamine; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100910130; LOC293862; protein FAM50A-like; RGD1560964; similar to XAP-5 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,246,533 - 157,253,650 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX157,246,533 - 157,253,650 (+)EnsemblGRCr8
mRatBN7.2X152,095,245 - 152,102,362 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX152,095,245 - 152,102,362 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX154,236,371 - 154,243,488 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,799,604 - 157,806,720 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,471,403 - 155,478,520 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,392,646 - 156,399,763 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,392,630 - 156,399,760 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl4104,949,597 - 104,956,714 (+)Ensemblrn6Rnor6.0
Rnor_5.01152,132,780 - 152,139,910 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X160,291,003 - 160,298,407NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1135,794,289 - 135,801,510 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22681889  


Genomics

Comparative Map Data
Fam50a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,246,533 - 157,253,650 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX157,246,533 - 157,253,650 (+)EnsemblGRCr8
mRatBN7.2X152,095,245 - 152,102,362 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX152,095,245 - 152,102,362 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX154,236,371 - 154,243,488 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,799,604 - 157,806,720 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,471,403 - 155,478,520 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,392,646 - 156,399,763 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,392,630 - 156,399,760 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl4104,949,597 - 104,956,714 (+)Ensemblrn6Rnor6.0
Rnor_5.01152,132,780 - 152,139,910 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X160,291,003 - 160,298,407NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1135,794,289 - 135,801,510 (-)NCBICelera
Cytogenetic MapXq37NCBI
FAM50A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X154,444,141 - 154,450,654 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX154,444,103 - 154,450,654 (+)Ensemblhg38GRCh38
GRCh37X153,672,488 - 153,679,002 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,325,702 - 153,332,190 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X153,236,211 - 153,242,700NCBI
CeleraX153,833,529 - 153,840,045 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX142,251,559 - 142,256,609 (+)NCBIHuRef
CHM1_1X153,584,110 - 153,590,638 (+)NCBICHM1_1
T2T-CHM13v2.0X152,680,649 - 152,687,163 (+)NCBIT2T-CHM13v2.0
Fam50a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X73,356,589 - 73,363,761 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX73,356,639 - 73,363,755 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X74,313,033 - 74,320,149 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX74,313,033 - 74,320,149 (+)Ensemblmm10GRCm38
MGSCv37X71,558,372 - 71,565,488 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X70,565,753 - 70,572,853 (+)NCBIMGSCv36mm8
CeleraX65,566,824 - 65,573,938 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.98NCBI
Fam50a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580941,729 - 947,686 (+)Ensembl
ChiLan1.0NW_004955580941,620 - 947,763 (+)NCBIChiLan1.0ChiLan1.0
FAM50A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X154,418,520 - 154,425,058 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X154,422,136 - 154,428,660 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,885,931 - 143,892,435 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,756,766 - 153,763,170 (+)NCBIPanPan1.1PanPan1.1panPan2
FAM50A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X122,148,234 - 122,158,172 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX122,148,282 - 122,154,807 (+)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.0X125,289,397 - 125,300,206 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX125,289,955 - 125,296,485 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X121,058,418 - 121,069,226 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X123,573,552 - 123,584,362 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X123,335,243 - 123,346,053 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Fam50a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,457,705 - 119,464,425 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049368091,195,430 - 1,205,340 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049368091,195,479 - 1,202,126 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAM50A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,967,510 - 124,973,483 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X124,967,821 - 124,973,487 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X143,612,016 - 143,686,125 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FAM50A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606566,672,617 - 66,679,433 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fam50a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946909,401 - 919,088 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624946909,398 - 918,972 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Fam50a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X128,315,005 - 128,321,823 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000073104, ENSRNOT00000075085
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat

Markers in Region
GDI1  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8X157,244,613 - 157,244,708 (+)Marker Load Pipeline
mRatBN7.2X152,093,324 - 152,093,420 (-)MAPPERmRatBN7.2
Rnor_6.0X156,401,588 - 156,401,683NCBIRnor6.0
Rnor_5.01152,141,735 - 152,141,830UniSTSRnor5.0
RGSC_v3.4X160,299,969 - 160,300,064UniSTSRGSC3.4
Celera1135,803,335 - 135,803,430UniSTS
Cytogenetic MapXq37.1-q37.2UniSTS
Cytogenetic MapXq37UniSTS
RH132835  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X152,101,125 - 152,101,744 (+)MAPPERmRatBN7.2
mRatBN7.2X152,101,125 - 152,101,744 (-)MAPPERmRatBN7.2
Rnor_6.0X156,393,264 - 156,393,882NCBIRnor6.0
Rnor_6.04104,955,470 - 104,956,088NCBIRnor6.0
Rnor_5.04169,680,159 - 169,680,777UniSTSRnor5.0
Rnor_5.01152,133,398 - 152,134,016UniSTSRnor5.0
RGSC_v3.44107,889,897 - 107,890,114UniSTSRGSC3.4
RGSC_v3.4X160,291,645 - 160,292,263UniSTSRGSC3.4
Celera1135,794,907 - 135,795,525UniSTS
Celera495,706,325 - 95,706,542UniSTS
Cytogenetic Map4q33UniSTS
Cytogenetic MapXq37UniSTS
RH134593  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X152,093,920 - 152,094,124 (-)MAPPERmRatBN7.2
Rnor_6.0X156,400,884 - 156,401,087NCBIRnor6.0
Rnor_5.01152,141,031 - 152,141,234UniSTSRnor5.0
RGSC_v3.4X160,299,265 - 160,299,468UniSTSRGSC3.4
Celera1135,802,631 - 135,802,834UniSTS
Cytogenetic MapXq37UniSTS
Cytogenetic MapXq37.1-q37.2UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 18 52 67 138 95 11 51 36 32 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000073104   ⟹   ENSRNOP00000065334
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4104,949,597 - 104,956,714 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000086921   ⟹   ENSRNOP00000071078
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX157,246,533 - 157,253,650 (+)Ensembl
mRatBN7.2 EnsemblX152,095,245 - 152,102,362 (+)Ensembl
Rnor_6.0 EnsemblX156,392,630 - 156,399,760 (-)Ensembl
RefSeq Acc Id: NM_001170573   ⟹   NP_001164044
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X157,246,533 - 157,253,650 (+)NCBI
mRatBN7.2X152,095,245 - 152,102,362 (+)NCBI
Rnor_6.0X156,392,646 - 156,399,763 (-)NCBI
Rnor_5.01152,132,780 - 152,139,910 (-)NCBI
Celera1135,794,289 - 135,801,510 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001164044 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68887 (Get FASTA)   NCBI Sequence Viewer  
  EDL84974 (Get FASTA)   NCBI Sequence Viewer  
  EDL84975 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000071078
  ENSRNOP00000071078.1
RefSeq Acc Id: NP_001164044   ⟸   NM_001170573
- UniProtKB: G3V9M8 (UniProtKB/TrEMBL),   A6KRQ9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071078   ⟸   ENSRNOT00000086921
Ensembl Acc Id: ENSRNOP00000065334   ⟸   ENSRNOT00000073104
Protein Domains
FAM50A/XAP5 C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V9M8-F1-model_v2 AlphaFold G3V9M8 1-339 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13702043
Promoter ID:EPDNEW_R12567
Type:initiation region
Name:Fam50a_1
Description:family with sequence similarity 50, member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X156,399,715 - 156,399,775EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560964 AgrOrtholog
BioCyc Gene G2FUF-628 BioCyc
Ensembl Genes ENSRNOG00000045790 Ensembl
  ENSRNOG00000058439 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000086921 ENTREZGENE
  ENSRNOT00000086921.3 UniProtKB/TrEMBL
InterPro FAM50A/XAP5_C UniProtKB/TrEMBL
  XAP5 UniProtKB/TrEMBL
KEGG Report rno:293862 UniProtKB/TrEMBL
NCBI Gene 293862 ENTREZGENE
PANTHER PROTEIN FAM50A UniProtKB/TrEMBL
  PTHR12722 UniProtKB/TrEMBL
Pfam XAP5 UniProtKB/TrEMBL
PhenoGen Fam50a PhenoGen
RatGTEx ENSRNOG00000045790 RatGTEx
  ENSRNOG00000058439 RatGTEx
UniProt A6KRQ9 ENTREZGENE, UniProtKB/TrEMBL
  B5DF16_RAT UniProtKB/TrEMBL
  G3V9M8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Fam50a  family with sequence similarity 50, member A  LOC100910130  protein FAM50A-like  Data merged from RGD:6500228 737654 PROVISIONAL
2012-07-05 LOC100910130  protein FAM50A-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-10-22 Fam50a  family with sequence similarity 50, member A  FAM50A  family with sequence similarity 50, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 FAM50A  family with sequence similarity 50, member A  RGD1560964_predicted  similar to XAP-5 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560964_predicted  similar to XAP-5 protein (predicted)  LOC293862  similar to XAP-5 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293862  similar to XAP-5 protein      Symbol and Name status set to provisional 70820 PROVISIONAL